Nadal's win in one hour and 43 minutes means that he has progressed to the final without dropping a set, Xinhua reported.
The unseeded Bautista Agut made Nadal work hard for his final place, but was unable to put enough pressure on the top seed's serve to ever look like causing an upset.
He will play Japan's Kei Nishikori in the final after the No. 10 seed prevented an all-Spanish final by defeating David Ferrer 7-6 (5), 5-7, 6-3 in one of the longest matches of the tournament.
The first set of the second semifinal went the way of the Japanese player after a tiebreak, while the second set was for the Spaniard, who was able to take the decisive break in Nishikori's final service game.
It was a long match, a typical clay court affair with long rallies and a lot of baseline play as both players looked to force their rival into a decisive error.
Nishikori has been in fine form of late and kept his nerve in the long final game as Ferrer saved several match points with the vocal support of the Madrid fans.
The women's final will be disputed between No. 8 seed Maria Sharapova and No. 4 seed Simona Halep.
Halep had to fight her way back from a set down on her way to a 6-7(4), 6-3, 6-2 win against Petra Kvitkova.
The opening set was tight but the Czech No. 5 seed began to struggle under the boiling sun on the center-court in the Caja Magica in Madrid in the second set, while Halep remained strong to book her place in the final.
Sharapova had come to Madrid on the back of success in Stuttgart and after defeating Li Na on Friday, the Russian was on the top of her game as she smashed her way past the No. 3 seed, Agnieszka Radwanska 6-1, 6-4 in just one hour and 10 minutes.